Note: some missiles, actually are really really really good at having direct, specific piercing action. Especially infantry rockets like RPG7 and panzerfaust for example. They have a cone with solid metal (usually copper),at the tip, and when you hit something the explosion melts the cone and sends it forward. Due to SCIENCE! the cone melts in such a way that it is a concentrated straight line of super heated metal that can pierce metal. This is why NATO vehicles have those grills on the side of transports. They don't stop the explosion, but they do make the liquid line have to move a further distance and less effective.
Considering that huge monsters with armor are more dangerous than little guys I am assuming that funnel missiles would be better suited for Samus rather than explosive missiles.